Abstract: We explore the effects of three-loop minimal supersymmetric standard model renormalisation group equation terms and some leading two-loop threshold corrections on gauge and Yukawa unification: each being one loop higher order than current public spectrum calculators. We also explore the effect of the higher order terms (often 2-3 GeV) on the lightest CP even Higgs mass prediction. We illustrate our results in the constrained minimal supersymmetric standard model. Neglecting threshold corrections at the grand unified scale, the discrepancy between the unification scale alpha(s) and the other two unified gauge couplings changes by 0.1% due to the higher order corrections and the difference between unification scale bottom-tau Yukawa couplings neglecting unification scale threshold corrections changes by up to 1%. The difference between unification scale bottom and top Yukawa couplings changes by a few percent. Differences due to the higher order corrections also give an estimate of the size of theoretical uncertainties in the minimal supersymmetric standard model spectrum. We use these to provide estimates of theoretical uncertainties in predictions of the dark matter relic density (which can be of order one due to its strong dependence on sparticle masses) and the LHC sparticle production cross-section (often around 30%). The additional higher order corrections have been incorporated into SOFTSUSY, and we provide details on how to compile and use the program. We also provide a summary of the approximations used in the higher order corrections. Program Summary Nature of problem: Calculating supersymmetric particle spectrum and mixing parameters in the minimal supersymmetric standard model. The solution to the renormalisation group equations must be consistent with boundary conditions on supersymmetry breaking parameters, as well as the weak-scale boundary condition on gauge couplings, Yukawa couplings and the Higgs potential parameters. Program title: SOFTSUSY Catalogue identifier: ADPMv50 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/ADPMv50.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 240528 No. of bytes in distributed program, including test data, etc.: 2597933 Distribution format: tar.gz Programming language: C++, Fortran. Computer: Personal computer. Operating system: Tested on Linux 3.4.6. Word size: 64 bits. Classification: 11.1, 11.6. External routines: At least GiNaC1.3.5 [1] and CLN1.3.1 (both freely obtainable from http://www.ginac.de). Does the new version supersede the previous version?: Yes Catalogue identifier of previous version: ADPMv40 Journal reference of previous version: Comput. Phys. Comm. 185 (2014) 2322 Solution method: Nested iterative algorithm. Reasons for new version: Extension to include additional two and three-loop terms. Summary of revisions: All quantities in the minimal supersymmetric standard model are extended to have three-loop renormalisation group equations (including 3-family mixing) in the limit of real parameters and some leading two-loop threshold corrections are incorporated to the third family Yukawa couplings and the strong gauge coupling. Restrictions: SOFTSUSY will provide a solution only in the perturbative regime and it assumes that all couplings of the model are real (i.e. CP-conserving). If the parameter point under investigation is non-physical for some reason (for example because the electroweak potential does not have an acceptable minimum), SOFTSUSY returns an error message. The higher order corrections included are for the real R-parity conserving minimal supersymmetric standard model (MSSM) only. Running time: A minute per parameter point. The tests provided with the package only take a few seconds to run.